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Title :   REDUCED FORM OF THE H PROTEIN FROM GLYCINE DECARBOXYLASE COMPLEX

Authors :   M. Faure, C. Cohen-Addad, M. Neuburger, R. Douce

Date :   10 Jan 00 (Deposition) - 04 Jul 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductases(Acting On Ch-Nh2 Donor), Glycine Decarboxylase, Mitochondria, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Faure, J. Bourguignon, M. Neuburger, D. Macherel, L. Sieker, R. Ober, R. Kahn, C. Cohen-Addad, R. Douce
Interaction Between The Lipoamide-Containing H-Protein And The Lipoamide Dehydrogenase (L-Protein) Of The Glycine Decarboxylase Multienzyme System. 2. Crystal Structure Of H- And L-Proteins
Eur. J. Biochem. V. 267 2890 2000
PubMed-ID: 10806386 | Reference-DOI: 10.1046/J.1432-1033.2000.01330.X
(for further references see the PDB file header)

Molecule 1 - H PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET-HM
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organ	:	LEAF
	Organelle	:	MITOCHONDRIA
	Organism Common	:	GARDEN PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888
	Synonym	:	GLYCINE CLEAVAGE SYSTEM H PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	RED	2	Ligand/Ion	DIHYDROLIPOIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	RED	1	Ligand/Ion	DIHYDROLIPOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	RED	1	Ligand/Ion	DIHYDROLIPOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:34 , LEU A:35 , LYS A:63 , GLU A:127	BINDING SITE FOR RESIDUE RED A 163
2	AC2	SOFTWARE	SER A:21 , VAL A:22 , GLU A:78 , LYS A:102 , HIS B:34 , LYS B:63	BINDING SITE FOR RESIDUE RED B 163

(no "SS Bond" information available for 1DXM)

(no "Cis Peptide Bond" information available for 1DXM)

(no "SAP(SNP)/Variant" information available for 1DXM)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_PEA	56-138	2	A:22-104 B:22-104
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_PEA	81-110	2	A:47-76 B:47-76

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_PEA	56-138	1	A:22-104 -
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_PEA	81-110	1	A:47-76 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_PEA	56-138	1	- B:22-104
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_PEA	81-110	1	- B:47-76

(no "Exon" information available for 1DXM)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with GCSH_PEA | P16048 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:131
                                    44        54        64        74        84        94       104       114       124       134       144       154       164 
             GCSH_PEA    35 SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVESVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELESLLGAKEYTKFCEEEDAAH 165
               SCOP domains d1dxma_ A: Protein H of glycine cleavage system                                                                                     SCOP domains
               CATH domains 1dxmA00 A:1-131  [code=2.40.50.100, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee..eeeeeehhhhhhhhh.eeeee............eeeeeee...eeeee....eeeeee.hhhhhh.hhhhhh.......eeeee.hhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BIOTINYL_LIPOYL  PDB: A:22-104 UniProt: 56-138                                     --------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------LIPOYL  PDB: A:47-76          ------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxm A   1 SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVESVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELESLLGAKEYTKFCEEEDAAH 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with GCSH_PEA | P16048 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:131
                                    44        54        64        74        84        94       104       114       124       134       144       154       164 
             GCSH_PEA    35 SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVESVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELESLLGAKEYTKFCEEEDAAH 165
               SCOP domains d1dxmb_ B: Protein H of glycine cleavage system                                                                                     SCOP domains
               CATH domains 1dxmB00 B:1-131  [code=2.40.50.100, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...eeeeee..eeeeeehhhhhhhhh.eeeee............eeeeeee...eeeee....eeeeee.hhhh...hhhhhh.......eeeee.hhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BIOTINYL_LIPOYL  PDB: B:22-104 UniProt: 56-138                                     --------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------LIPOYL  PDB: B:47-76          ------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxm B   1 SNVLDGLKYAPSHEWVKHEGSVATIGITDHAQDHLGEVVFVELPEPGVSVTKGKGFGAVESVKATSDVNSPISGEVIEVNTGLTGKPGLINSSPYEDGWMIKIKPTSPDELESLLGAKEYTKFCEEEDAAH 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Barrel-sandwich hybrid (185)

Superfamily: Single hybrid motif (49)

Family: Biotinyl/lipoyl-carrier proteins and domains (40)

Protein domain: Protein H of glycine cleavage system (11)

Pea (Pisum sativum) [TaxId: 3888] (3)

1a	d1dxma_	A:
1b	d1dxmb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.100, no name defined] (113)

Garden pea (Pisum sativum) (1)

1a	1dxmA00	A:1-131
1b	1dxmB00	B:1-131

(no "Pfam Domain" information available for 1DXM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GCSH_PEA | P16048)

biological process
	GO:0019464	glycine decarboxylation via glycine cleavage system	The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
	GO:0005960	glycine cleavage complex	A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	GCSH_PEA \| P16048	:	1hpc 1htp

1hpc	H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM, AMINOMETHYLTRANSFERASE (E.C.1.4.4.2) FROM GARDEN PEA (PISUM SATIVUM)
1htp	H-PROTEIN (E.C.1.4.4.2) COMPLEXED WITH LIPOIC ACID CHARGED IN METHYLAMINE FROM PEA (PISUM SATIVUM)

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